[BioC] Change M-value calculation from red/green to green/red

[Gordon K Smyth]

Dear Torsten,

There is no need to fool the software as to the real nature of your data. 
Please do not do this.

Simply use

   modelMatrix(targets, ref="Ref")

where "Ref" is the name of your reference sample.  Then limma will compute 
all quantities correctly relative to the reference regardless of what dye 
was used.

Best wishes
Gordon


> Date: Wed, 10 Jun 2009 11:07:23 +0100
> From: "michael watson \(IAH-C\)" <michael.watson at bbsrc.ac.uk>
> Subject: Re: [BioC] Change M-value calculation from red/green to
> 	green/red
> To: "Torsten Waldminghaus" <Torsten.Waldminghaus at rr-research.no>,
> 	<bioconductor at stat.math.ethz.ch>
>
> Multiply by -1
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Torsten
> Waldminghaus
> Sent: 10 June 2009 10:59
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Change M-value calculation from red/green to green/red
>
> Dear all,
>
> I started using the limma library to deal with microarray data. The
> available functions are really helpful to do normalization like this:
>
> RG <- read.maimages(files,"agilent")
> RG.b <- backgroundCorrect(RG,method="minimum")
> MA.p <-normalizeWithinArrays(RG.b,method="loess")
> MA.pAq <- normalizeBetweenArrays(MA.p, method="Aquantile")
>
> However, in my experiments I had the reference sample labeled in green
> so I would like to have M-values calculated as M=log2G-log2R instead of
> M=log2R-log2G. Is there any simple way to do this?
>
> Thanks for any help,
> Torsten
>
> Torsten Waldminghaus
> Department of Cell Biology
> Institute for Cancer Research
> Rikshospitalet-Radiumhospitalet-HF
> Ullernchaussen 70
> 0310 Oslo
> tel: 47-22935973
> fax: 47-22934580
> e-mail: Torsten.Waldminghaus at rr-research.no
> http://openwetware.org/wiki/User:Torsten_Waldminghaus